Hailing from the outer regions of space, from the Dark Gas Nebula in the Orion Constellation, a microscopic alien life form attached itself to the passing Ikeya Comet. This hunk of rock would eventually bypass Earth, and bring to the planet a new monster. However, the creature's arrival did not go unnoticed. While on a routine catch for shrimp, a fisherman, by the name of Gohei, discovers what appears to be a new breed of tadpole. Gohei immediately takes his finding to Professor Yano for study. However, before Yano can thoroughly study the specimen, a beast, resembling a giant version of the mysterious tadpole, engages two ships out at sea, sinking both in mere minutes. Fearful that their might be a connection between the sample and this new menace, Yano decides to investigate the common source of the occurrences: the nearby bay. The Professor dons his scuba gear, and submerges himself in the bay in search of clues, while his son, Ken Yano, awaits his return. However, while waiting for his father on shore, Ken is attacked by a bus sized tadpole. Ken fights back with his knife, tearing through the monster's stomach with no effect. Ken is left dumbfounded, though, as the mammoth tadpole spares him and returns out to sea. Once back underwater, the monster happens upon Professor Yano scuba diving, and is far less merciful. The Professor is brutally attacked by the monster tadpole, left with the right side of his face horrible deformed.

After Yano is brought back to his house, so that he can nurse his injury, the Professor immediately continues his studies on the new organism. Through his observations, Yano makes a startling discovery. As long as the animal is moist, and has an ample supply of pollution to feed on, it could grow indefinitely. However, Yano also discovers another horrifying fact. When the creature was cut in half, both halves where not only able to survive, but regroup and form a new larger body. It's this reason he speculated to his son, whom now dubbed the mysterious monster Hedorah after the sludge it lives in, why the beast was able to grow so fast.

Defying all natural laws of science, Hedorah evolved from a fish-like tadpole to a four legged monster in but a few days. Taking full advantage of this new powerful form, the smog monster waded onto the land to further its size and strength. Hedorah lumbered onto the gas expelling smokestacks of the nearby factories around Sagami Bay. Unfortunately, its feast was cut short by the sudden appearance of Godzilla. Angered by this interruption, Hedorah immediately attacked, leaping onto the saurian in a rage of malice. Though Godzilla fought back, his attacks proved futile. His clawed fists punched through the creature's flesh with no harm, and his beam proved even less effective. However, during the clash, as Godzilla swung Hedorah around, pieces of its flesh broke loose and were sent hurtling through a nearby window of a night club. The shambling blob took on a life of its own and moved through the establishment with authority. The rolling mass killed four people, but for some peculiar reason, spared the life of a kitten. However, it quickly disappeared into the night. Shortly after, the brief clash of giants ceased, with Hedorah diving backing into the mucky sea. Godzilla gave chase, diving in after the Smog Monster, but was unable to follow.

It wasn't until the next morning did the thing make itself known again. The offspring that was unleashed in the club the night before, now grown, attacked a street that was filled with cars caught in a traffic jam. Feeding off the polluting machines, the creature was able to gain enough strength to later join with the much larger Hedorah from the previous night. Together they flew to Mount Fuji, and morphed into a 60 meter tall biped giant. Unfortunately for Hedorah, the military, along with Godzilla, were waiting. Unified, mankind and the giant leviathan trapped the tower of sludge between two electrodes that dried him out. Seeing defeat at hand, the Hedorahs were forced to separate. The smaller Hedorah flew away, after Godzilla tore the eyes out of the much larger Hedorah, killing it instantly. Godzilla, using his breath as a means of jet propulsion, managed to catch the fleeing alien. The two titans fought a final time, with Godzilla ending victorious. The nuclear behemoth picked up the easily defeated Hedorah and flew back to the electrodes; afterwards, using his ray at the sheets of metal, the bouncing energy was more than enough to dry out the smaller sludge monster, killing the last of the species.

After escaping Godzilla's wrath, the larger Hedorah was pressed to further its evolution in order to continue its growth. Changing into a saucer like flying form, the invader sought out the gasoline tanks of the Japanese oil refinery. Nevertheless, though, Godzilla was waiting, and waded into the refinery area to battle Hedorah once again. Surprisingly, this time around, the smog monster took the victory, and left the reptile giant choking on the ground. The flying horror then decided to move further inland. In its destructive wake, over sixteen hundred people on the south side of Fuji City perished. All victims of Hedorah's sulfuric acid mist.

Meanwhile, Professor Yano discovers that the Hedorah creature can be killed by drying it out. The authorities are immediately alerted, and begin preparations for Hedorah's next strike. Night replaces the light, and it is revealed that the smaller Hedorah, who had wrecked havoc at a night club the night before, had joined up with the larger one. Growing to the size of over sixty meters, the now towering animal traveled to Osaka, and then to Mount Fuji. On the mountain, though, a few dozen teenagers are found partying. They were throwing a bonfire to protest the despair that the newly arrived alien was bringing to the world. As luck would have it though, before Hedorah could kill them all, it is was stopped short by Godzilla, setting the stage for their final clash.

After witnessing the force of Godzilla, the two Hedorahs united to form a much more powerful body. Evolving now to a sixty meter tall biped giant, the cosmic murderer faced the seething Godzilla along the slopes of Mt. Fuji. The pair battled back and forth, but the nuclear giant couldn't stand against Hedorah's corrosive muck and crimson eye beams. The world's hero was toppled, and carried away by the alien, as it changed back to its horrific flying form. Godzilla was dumped into a pit and left for dead, while Hedorah began to make its way back across the mountain.

During the battle, the military began to set up camp on the mountain. They prepared two giant electrodes which were 40 meters high and 60 meters wide. It was hoped, that, with the headlights of a few jeeps, they could lure Hedorah between the electrodes and dry it out. Unfortunately, during the monsters' fight, one of the power lines, that feed the massive machines their power, was taken out. Luckily for humanity, Godzilla appeared on the scene as Hedorah was led between the manmade structures. Blasting his radioactive breath at one of the electrodes, the energy was bounced back and forth between, trapping Hedorah in a vortex of utter pain and agony. Dying from dehydration, Godzilla took little pity and shoved its clawed hands into the chaotic beasts fleshy mass. Ripping free, two orb like eyes, the scaly behemoth tore the destined to be hellish demons from the near motionless body. Then, making sure that the job was finished, the titan let loose with another blast at the electrodes, drying out the eyes.